A microenvironment-sensitive fluorescent pyrimidine ribonucleoside analogue: synthesis, enzymatic incorporation, and fluorescence detection of a DNA abasic site

Base-modified fluorescent ribonucleoside-analogue probes are valuable tools in monitoring RNA structure and function because they closely resemble the structure of natural nucleobases. Especially, 2-aminopurine, a highly environment-sensitive adenosine analogue, is the most extensively utilized fluorescent nucleoside analogue. However, only a few isosteric pyrimidine ribonucleoside analogues that are suitable for probing the structure and recognition properties of RNA molecules are available. Herein, we describe the synthesis and photophysical characterization of a small series of base-modified pyrimidine ribonucleoside analogues derived from tagging indole, N-methylindole, and benzofuran onto the 5-position of uracil. One of the analogues, based on a 5-(benzofuran-2-yl)pyrimidine core, shows emission in the visible region with a reasonable quantum yield and, importantly, displays excellent solvatochromism. The corresponding triphosphate substrate is effectively incorporated into oligoribonucleotides by T7 RNA polymerase to produce fluorescent oligoribonucleotide constructs. Steady-state and time-resolved spectroscopic studies with fluorescent oligoribonucleotide constructs demonstrate that the fluorescent ribonucleoside photophysically responds to subtle changes in its environment brought about by the interaction of the chromophore with neighboring bases. In particular, the emissive ribonucleoside, if incorporated into an oligoribonucleotide, positively reports the presence of a DNA abasic site with an appreciable enhancement in fluorescence intensity. The straightforward synthesis, amicability to enzymatic incorporation, and sensitivity to changes in the microenvironment highlight the potential of the benzofuran-conjugated pyrimidine ribonucleoside as an efficient fluorescent probe to investigate nucleic acid structure, dynamics, and recognition events.     

从分子碎片到活性位：分子筛催化材料的原位、共振紫外拉曼光谱研究

在过去的近十年中,各种新型原位表征技术和反应器设计被应用于多相催化过程和催化材料的合成研究中,并获得了许多新认识．特别是最近几年,利用原位、共振拉曼光谱技术对分子筛合成关键物种检测、杂原子分子筛催化活性位的研究取得了一系列进展．这些技术的应用使得从分子水平认识复杂的多孔材料成为可能：从合成初期碎片基元检测、碎片相互连接的关键化学键到预组装类微孔结构;从高度隔离过渡金属中心到配位化学键断裂生成活性中间物种,再到完成催化反应循环．这为设计特定功能和结构的催化材料及高选择性的活性中心奠定了坚实的基础．     

Competitive Assay for Theophylline Based on an Abasic Site‐Containing DNA Duplex Aptamer and a Fluorescent Ligand

A fluorescence assay for theophylline, one of the common drugs for acute and chronic asthmatic conditions, has been developed based on an abasic site‐containing DNA duplex aptamer (AP aptamer) in combination with an abasic site‐binding fluorescent ligand, riboflavin. The assay is based on the competitive binding of theophylline and riboflavin at the abasic (AP) site of the AP aptamer. In the absence of theophylline, riboflavin binds to the receptor nucleotide opposite the AP site, which leads to fluorescence quenching of the riboflavin. Upon addition of theophylline, competitive binding occurs between theophylline and riboflavin, which results in an effective fluorescence restoration due to release of riboflavin from the AP site. From an examination of the optimization of the AP aptamers, the complex of riboflavin with a 23‐mer AP aptamer (5′‐TCT GCG TCC AGX GCA ACG CAC AC‐3′/5′‐GTG TGC GTT GCC CTG GAC GCA GA‐3′; X : the AP site (Spacer C3, a propylene residue)) possessing cytosine as a receptor nucleotide was found to show a selective and effective fluorescence response to theophylline; the limit of detection for theophylline was 1.1 μM . Furthermore, fluorescence detection of theophylline was successfully demonstrated with high selectivity in serum samples by using the optimized AP aptamer and riboflavin.     

金团簇二十面体结构融合过程中其催化活性的演变

近年来,由有机配体保护的原子精确金属团簇在合成方面已取得了重要进展,其独特的原子结构对一些化学反应产生独特的催化效果.原子精确的团簇催化剂明显不同于纳米颗粒催化剂和单原子催化剂,是一种关联均相和多相的、原子数目确定、尺寸均一、结构精确的新型催化剂.从原子尺度上精确构筑团簇催化剂,探究亚纳米尺度的微观结构对催化性能的影响...     

氮掺杂纳米管包覆金属钴催化苯甲醇和苯胺一步N-烷基化反应

通过直接热解三聚氰胺、硝酸钴和葡萄糖混合物制备氮掺杂碳纳米管包覆金属钴催化剂(Co@NCNT).Co@NCNT具有较大的比表面积、均匀的氮分布以及包覆结构.在苯甲醇和苯胺一步法N-烷基化反应中Co@N CNT具有较高的催化活性,且循环4次反应活性没有明显的变化.控制实验和中毒实验表明金属Co和N对催化活性起着重要的作用,同时金属Co是中间产物N-苄叉苯胺加氢的主要活性位.     

Machine Learning Approaches for Metalloproteins

Metalloproteins are a family of proteins characterized by metal ion binding, whereby the presence of these ions confers key catalytic and ligand-binding properties. Due to their ubiquity among biological systems, researchers have made immense efforts to predict the structural and functional roles of metalloproteins. Ultimately, having a comprehensive understanding of metalloproteins will lead to tangible applications, such as designing potent inhibitors in drug discovery. Recently, there has been an acceleration in the number of studies applying machine learning to predict metalloprotein properties, primarily driven by the advent of more sophisticated machine learning algorithms. This review covers how machine learning tools have consolidated and expanded our comprehension of various aspects of metalloproteins (structure, function, stability, ligand-binding interactions, and inhibitors). Future avenues of exploration are also discussed.     

A Mössbauer study of octahedral site symmetries in systems Co x Mn3−x−y Fe y O4 and Ni x Mn3−x−y Fe y O4

A Mössbauer study of cation distribution in systems Co _x Mn_3?x?y Fe _y O₄ and Ni _x Mn_3?x?y Fe _y O₄ has been made. It has been found that in both systems all specimens withy<0.6 value exhibit quadrupole doublets corresponding to site symmetries Fe³⁺(I) and Fe³⁺(II) of octahedral site. As more and more cobalt or nickel is introduced into the matrix the intensity of the inner quadrupole doublet increases while on introducing iron that of the outer quadrupole doublet increases. After a certain concentration of iron the inner doublet starts becoming more intense. It is suggested that this arises possibly from the substitution of cations in the second co-ordination sphere of Fe³⁺(I) and Fe³⁺(II) sites. Fory>0.6 the Mössbauer spectra show relaxation effects.     

Origin and Prediction of Highly Specific Bond Cleavage Sites in the Thermal Activation of Intact Protein Ions

Predicting the fragmentation patterns of proteins would be beneficial for the reliable identification of intact proteins by mass spectrometry. However, the ability to accurately make such predictions remains elusive. An approach to predict the specific cleavage sites in whole proteins resulting from collision-induced dissociation by use of an improved electrostatic model for calculating the proton configurations of highly-charged protein ions is reported. Using ubiquitin, cytochrome c, lysozyme and β-lactoglobulin as prototypical proteins, this approach can be used to predict the fragmentation patterns of intact proteins. For sufficiently highly charged proteins, specific cleavages occur near the first low-basicity amino acid residues that are protonated with increasing charge state. Hybrid QM/QM′ (QM=quantum mechanics) and molecular dynamics (MD) simulations and energy-resolved collision-induced dissociation measurements indicated that the barrier to the specific dissociation of the protonated amide backbone bond is significantly lower than competitive charge remote fragmentation. Unlike highly charged peptides, the protons at low-basicity sites in highly charged protein ions can be confined to a limited sequence of low-basicity amino acid residues by electrostatic repulsion, which results in highly specific fragmentation near the site of protonation. This research suggests that the optimal charge states to form specific sequence ions of intact proteins in higher abundances than the use of less specific ion dissociation methods can be predicted a priori.     

Optimization of Active Sites via Crystal Phase,Composition, and Morphology for Efficient Low-Iridium Oxygen Evolution Catalysts

Reducing the amount of iridium in oxygen evolution electrocatalysts without compromising their catalytic performances is one of the major requirements in proton-exchange-membrane water electrolyzers. Herein, with the help of theoretical studies, we show that anatase-type TiO₂-IrO₂ solid solutions possess more active iridium catalytic sites for the oxygen evolution reaction (OER) than IrO₂, the benchmark OER catalyst. Note that the same is not observed for their rutile-type counterparts. However, owing to their thermodynamic metastability, anatase-type TiO₂-IrO₂ solid solutions are generally hard to synthesize. Our theoretical studies demonstrate that such catalytically active anatase-type solid-solution phases can be created in situ on the surfaces of readily available SrTiO₃-SrIrO₃ solid solutions during electrocatalysis in acidic solution as the solution can etch away Sr atoms. We experimentally show this with porous SrTiO₃-SrIrO₃ solid-solution nanotubes synthesized by a facile synthetic route that contain 56 % less iridium than IrO₂ yet show an order of magnitude higher apparent catalytic activity for OER in acidic solution.     

4fN-15d energy levels of lanthanides: aquasi-angular-momentum approach and its application to Cs2NaYF6:Er3+

<正>The spin-orbit interaction of the 5d electron needs to be taken into account to give the proper energy structure for the 4f^N-15d configuration of heavy lanthanide ions occupying a site with ligands forming an octahedron.This paper derives theoretical results for the energy structure by treating the t₂ orbitals as quasi p orbitals and then using angular-momentum coupling techniques.An analytic expression for the electric dipole absorption line strengths between 4f^N multiplets and 4f^N-15d states is given in terms of various angular-momentum quantum numbers and re-coupling coefficients.The result is then applied to interpret the excitation spectrum of Cs₂NaYF₆:Er³⁺.The high-spin and low-spin states of Cs₂NaYF₆:Er³⁺ are discussed in terms of the wavefunctions obtained by using the developed theoretical model.